Articles

FANTOM4

FANTOM4: Systems biology of a leukemia transcriptome and its regulation

This special collection of articles are the companion papers for the three FANTOM4 papers published with Nature Genetics.

FANTOM4 has used genome-wide expression profiling to measure the expression dynamics of promoter usage, mRNAs, microRNAs and other small non-coding RNAs throughout a time course of differentiation in the acute myeloid leukemia cell line THP-1. Of particular interest was the extensive use of deepCAGE (a new deep sequencing application) to identify active promoters and their expression dynamics. Computational analysis, chromatin immunoprecipitation and perturbation experiments have then been used to build network models of the transcription factors and miRNAs, their targets and their role in differentiation and maintenance of the undifferentiated state.

CAGE tag mapping of transcription start sites across different human tissues shows that genomic regulatory blocks have unique features that are the likely cause of their ability to respond to regulatory inputs from very long distances.